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The Second Doctor and Jamie McCrimmon land the TARDIS on board Space Station Chimera in the Third Zone on a mission for the Time Lords, who have also installed a teleport control on the TARDIS. The Doctor explains that the station is a research facility and that they have to talk to Dastari, the Head of Projects. The TARDIS materialises in the station kitchen, where they meet Shockeye, the station cook.

The TARDIS materialises on the station, but the smell of decay and death is everywhere. The station computer demands that the Doctor leave and, when he refuses, tries to kill him and Peri by depressurising the passageway.

Meanwhile, the Sixth Doctor and Jamie are in the cellar, where the Doctor examines the Kartz-Reimer module, a prototype time machine modelled on Time Lord technology. He explains to Jamie that once the briode nebuliser of the module is primed with his symbiotic nuclei — the Rassilon Imprimatur — it will be safe for anyone to use. Unfortunately, the Sontarans have heard him. Outside, Shockeye catches Peri. She falls, and Shockeye leans over her body.

Shockeye knocks Peri out and brings her back to the hacienda kitchen. In the cellar, Stike threatens to kill Jamie unless the Sixth Doctor gets into the module and primes it with his symbiotic print, and the Doctor does so. Stike is about to execute Jamie anyway, but Jamie stabs Stike's leg with a concealed knife, and the Doctor and he run off upstairs, where they find the Second Doctor. Before they can release the Second Doctor and escape the hacienda, however, Shockeye shows up with the unconscious Peri. The Second Doctor feigns unconsciousness while the others hide.

The Second Doctor uses a Stattenheim remote control to summon his TARDIS. He and Jamie say their goodbyes and leave. As the Sixth Doctor and Peri make their way back to their own TARDIS, the Doctor tells her that from now on, it will be a healthy vegetarian diet for both of them.

Working titles for this story included The Kraglon Inheritance and The Androgum Inheritance.[2] Robert Holmes, a vegetarian, wrote the serial as an allegory about meat-eating, hunting and butchering. "Androgum" is an anagram of "gourmand".[3] Elements from Robert Holmes's aborted project The Six Doctors were carried over to this story (as the production subtitles for the DVD release reveal).

Holmes's original brief from producer John Nathan-Turner was to write a serial taking place in New Orleans, involving the Sontarans, the Second Doctor and Jamie, but the setting had to be changed to Spain instead when the expected funding for location filming in the United States fell through. Holmes was particularly disappointed that much of the humour involving the differences between Britain and America was lost in the rewrite. The only hint we get of this humour is in Episode 1, when the Sixth Doctor looks at Peri and says that Columbus "has a lot to answer for".[2]

According to the DVD commentary track, location filming was plagued by numerous small problems, including high heat that caused make-up to melt, a three-day delay to replace Troughton and Pearce's wigs (which had somehow got lost in shipping), Carmen Gómez' refusal to wear a costume designed for her, and a local stunt man (the truck driver) who refused to perform his stunt as it had been choreographed. Pearce also says that she was a last-minute replacement for another, unspecified actress who had to drop out of the production. A filmed scene with Oscar and Anita in the olive grove was discovered to have been ruined by a scratch on the negative, so Saxon and Gómez, who had already returned to England, had to be quickly brought back to Spain at considerable expense. This was the latest of a number of stories which included location filming outside the United Kingdom, starting with City of Death. Discounting the 1996 TV movie which was produced entirely in Canada, and the 2007 episode "Daleks in Manhattan" which included some second unit footage shot in New York City, another regular series episode would not be substantially filmed outside the UK until "The Fires of Pompeii" which was broadcast in 2008.[citation needed]

During the transmission of the story, the news that the series would be put on hiatus for a year was announced.[citation needed] Much controversy still surrounds this period and action, with disputes over whether or not the series was facing cancellation outright at this stage, and the roles of various BBC officials such as BBC One controller Michael Grade and Head of Drama Serials Jonathan Powell.[citation needed]

The Two Doctors was one of several stories from this era to provoke controversy over its depiction of violence. In 1985, Australasian Doctor Who Fan Club president Tony Howe criticised the murder of Oscar with a kitchen knife as being an instance of "sick, shock violence" that was present for "cheap shock value only".[7]

The novelisation of this serial, by Robert Holmes, was published in hardback and paperback in August 1985 as the 100th Doctor Who release by Target Books. This was Holmes's only complete novelisation and seeks to clear up some of the continuity errors in the original broadcast. With a gold foil-embossed cover, it was billed on release as the 100th novelisation and featured an introduction by John Nathan-Turner.

The Two Doctors was released on VHS in November 1993. It was released on DVD in the UK in September 2003 in a two-disc set as part of the Doctor Who 40th Anniversary Celebration releases, representing the Colin Baker years, with many extra features, including the Jim'll Fix It sketch A Fix with Sontarans. The DVD contains a full-length commentary provided by director Peter Moffatt and actors Colin Baker, Nicola Bryant, Frazer Hines, and Jacqueline Pearce. The DVD was subsequently incorporated into the box setBred for War, along with The Time Warrior, The Sontaran Experiment and The Invasion of Time. Following the sexual abuse accusations regarding Jimmy Savile, the DVD was withdrawn from sale but has since been rereleased with the sketch removed.[8] The BBC has made the serial available for download on Apple iTunes. It was released in issue 45 of Doctor Who DVD Files.